def test_scratch_container(self):
data = TimeSeries(
name='test_ts',
data=[1, 2, 3, 4, 5],
unit='unit',
timestamps=[1.1, 1.2, 1.3, 1.4, 1.5]
)
nwbfile = NWBFile(
session_description='test',
identifier='test',
session_start_time=self.start_time,
file_create_date=self.create_date
)
nwbfile.add_scratch(data)
self.writer = NWBHDF5IO(self.filename, mode='w')
self.writer.write(nwbfile)
self.writer.close()
self.reader = NWBHDF5IO(self.filename, mode='r')
self.read_nwbfile = self.reader.read()
ret = self.read_nwbfile.get_scratch('test_ts')
self.assertContainerEqual(data, ret)
self.validate()
def test_scratch_convert_DataFrame_table_desc(self):
"""Test round trip convert of DataFrame with a table description"""
data = pd.DataFrame(data={
'col1': [1, 2, 3, 4],
'col2': ['a', 'b', 'c', 'd']
})
case = 'dataframe_desc'
self.filename = 'test_scratch_%s.nwb' % case
description = 'a file to test writing and reading a scratch data of type %s' % case
identifier = 'TEST_scratch_%s' % case
nwbfile = NWBFile(description,
identifier,
self.start_time,
file_create_date=self.create_date)
nwbfile.add_scratch(data, name='foo', table_description='my_table')
self.writer = NWBHDF5IO(self.filename, mode='w')
self.writer.write(nwbfile)
self.writer.close()
self.reader = NWBHDF5IO(self.filename, mode='r')
self.read_nwbfile = self.reader.read()
ret = self.read_nwbfile.get_scratch('foo', convert=False)
ret_df = ret.to_dataframe()
self.assertEqual(ret.description, 'my_table')
assert_array_equal(data.values, ret_df.values)
assert_array_equal(data.index.values, ret_df.index.values)
self.validate()
def _test_scratch_container(self, validate=True, **kwargs):
data = TimeSeries('test_ts', [1, 2, 3, 4, 5],
unit='unit',
timestamps=[1.1, 1.2, 1.3, 1.4, 1.5])
nwbfile = NWBFile('test',
'test',
self.start_time,
file_create_date=self.create_date)
nwbfile.add_scratch(data, **kwargs)
self.writer = NWBHDF5IO(self.filename, mode='w')
self.writer.write(nwbfile)
self.writer.close()
self.reader = NWBHDF5IO(self.filename, mode='r')
self.read_nwbfile = self.reader.read()
ret = self.read_nwbfile.get_scratch('test_ts')
self.assertContainerEqual(data, ret)
if validate:
self.validate()
class TestScratchData(TestCase):
def setUp(self):
self.nwbfile = NWBFile(
session_description='a file to test writing and reading scratch data',
identifier='TEST_scratch',
session_start_time=datetime(2017, 5, 1, 12, 0, 0, tzinfo=tzlocal())
)
def test_constructor_list(self):
sd = ScratchData(
name='foo',
data=[1, 2, 3, 4],
description='test scratch',
)
self.assertEqual(sd.name, 'foo')
self.assertListEqual(sd.data, [1, 2, 3, 4])
self.assertEqual(sd.description, 'test scratch')
def test_add_scratch_int(self):
ret = self.nwbfile.add_scratch(2, name='test', description='test data')
self.assertIsInstance(ret, ScratchData)
self.assertEqual(ret.name, 'test')
self.assertEqual(ret.data, 2)
self.assertEqual(ret.description, 'test data')
self.assertIs(ret.parent, self.nwbfile)
self.assertEqual(self.nwbfile.get_scratch('test'), 2)
def test_add_scratch_list(self):
self.nwbfile.add_scratch([1, 2, 3, 4], name='test', description='test data')
assert_array_equal(self.nwbfile.get_scratch('test'), np.array([1, 2, 3, 4]))
def test_add_scratch_ndarray(self):
self.nwbfile.add_scratch(np.array([1, 2, 3, 4]), name='test', description='test data')
assert_array_equal(self.nwbfile.get_scratch('test'), np.array([1, 2, 3, 4]))
def test_add_scratch_list_no_name(self):
msg = ('A name is required for NWBFile.add_scratch when adding a scalar, numpy.ndarray, '
'list, tuple, or pandas.DataFrame as scratch data.')
with self.assertRaisesWith(ValueError, msg):
self.nwbfile.add_scratch([1, 2, 3, 4])
def test_add_scratch_ndarray_no_description(self):
msg = ('A description is required for NWBFile.add_scratch when adding a scalar, numpy.ndarray, '
'list, tuple, or pandas.DataFrame as scratch data.')
with self.assertRaisesWith(ValueError, msg):
self.nwbfile.add_scratch(np.array([1, 2, 3, 4]), name='test')
def test_add_scratch_dataframe(self):
data = pd.DataFrame(data={'col1': [1, 2, 3, 4], 'col2': ['a', 'b', 'c', 'd']})
self.nwbfile.add_scratch(data, name='test', description='my_table')
assert_array_equal(data.values, self.nwbfile.get_scratch('test').values)
assert_array_equal(data.index.values, self.nwbfile.get_scratch('test').index.values)
def test_add_scratch_dataframe_no_description(self):
data = pd.DataFrame(data={'col1': [1, 2, 3, 4], 'col2': ['a', 'b', 'c', 'd']})
msg = ('A description is required for NWBFile.add_scratch when adding a scalar, numpy.ndarray, '
'list, tuple, or pandas.DataFrame as scratch data.')
with self.assertRaisesWith(ValueError, msg):
self.nwbfile.add_scratch(data, name='test')
def test_add_scratch_container(self):
data = TimeSeries(name='test_ts', data=[1, 2, 3, 4, 5], unit='unit', timestamps=[1.1, 1.2, 1.3, 1.4, 1.5])
self.nwbfile.add_scratch(data)
self.assertIs(self.nwbfile.get_scratch('test_ts'), data)
self.assertIs(self.nwbfile.scratch['test_ts'], data)
def test_add_scratch_container_name(self):
data = TimeSeries(name='test_ts', data=[1, 2, 3, 4, 5], unit='unit', timestamps=[1.1, 1.2, 1.3, 1.4, 1.5])
msg = ('The name argument is ignored when adding an NWBContainer, ScratchData, or '
'DynamicTable to scratch.')
with self.assertWarnsWith(UserWarning, msg):
self.nwbfile.add_scratch(data, name='Foo')
self.assertIs(self.nwbfile.get_scratch('test_ts'), data)
self.assertIs(self.nwbfile.scratch['test_ts'], data)
def test_add_scratch_container_description(self):
data = TimeSeries(name='test_ts', data=[1, 2, 3, 4, 5], unit='unit', timestamps=[1.1, 1.2, 1.3, 1.4, 1.5])
msg = ('The description argument is ignored when adding an NWBContainer, ScratchData, or '
'DynamicTable to scratch.')
with self.assertWarnsWith(UserWarning, msg):
self.nwbfile.add_scratch(data, description='test scratch')
self.assertIs(self.nwbfile.get_scratch('test_ts'), data)
self.assertIs(self.nwbfile.scratch['test_ts'], data)
def test_add_scratch_scratchdata(self):
data = ScratchData(name='test', data=[1, 2, 3, 4, 5], description='test description')
self.nwbfile.add_scratch(data)
self.assertIs(data.parent, self.nwbfile)
self.assertIs(self.nwbfile.get_scratch('test', convert=False), data)
self.assertIs(self.nwbfile.scratch['test'], data)
def test_add_scratch_dynamictable(self):
data = DynamicTable(name='test', description='description')
self.nwbfile.add_scratch(data)
self.assertIs(self.nwbfile.get_scratch('test', convert=False), data)
self.assertIs(self.nwbfile.scratch['test'], data)
def test_get_scratch_list_convert_false(self):
self.nwbfile.add_scratch([1, 2, 3, 4], name='test', description='test description')
self.assertTrue(isinstance(self.nwbfile.get_scratch('test', convert=False), ScratchData))
self.assertTrue(isinstance(self.nwbfile.scratch['test'], ScratchData))
self.assertEqual(self.nwbfile.scratch['test'].data, [1, 2, 3, 4])
def test_get_scratch_df_convert_false(self):
data = pd.DataFrame(data={'col1': [1, 2, 3, 4], 'col2': ['a', 'b', 'c', 'd']})
self.nwbfile.add_scratch(data, name='test', description='my_table')
self.assertTrue(isinstance(self.nwbfile.get_scratch('test', convert=False), DynamicTable))
self.assertTrue(isinstance(self.nwbfile.scratch['test'], DynamicTable))
self.assertEqual(self.nwbfile.scratch['test'].description, 'my_table')
